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Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma

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Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma Published OnlineFirst June 6, 2017; DOI: 10.1158/2159-8290.CD-17-0419 RESEARCH BRIEF Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma Olga Kondrashova 1 , 2 , Minh Nguyen 3 , Kristy Shield-Artin 1 , 2 , Anna V. Tinker 4 , Nelson N.H. Teng 5 , Maria I. Harrell 6 , Michael J. Kuiper 7 , Gwo-Yaw Ho 1 , 2 , 8 , Holly Barker1,2 , Maria Jasin 9 , Rohit Prakash 9 , Elizabeth M. Kass 9 , Meghan R. Sullivan 10 , Gregory J. Brunette 10 , Kara A. Bernstein 10 , Robert L. Coleman 11 , Anne Floquet 12 , Michael Friedlander 13 , Ganessan Kichenadasse 14 , David M. O’Malley 15 , Amit Oza 16 , James Sun 17 , Liliane Robillard3 , Lara Maloney 3 , David Bowtell on behalf of the AOCS Study Group 18,19, 20 , Heidi Giordano3 , Matthew J. Wakefi eld 1 , 7 , Scott H. Kaufmann 21 , Andrew D. Simmons 3 , Thomas C. Harding 3 , Mitch Raponi 3 , Iain A. McNeish 22 , Elizabeth M. Swisher 6 , Kevin K. Lin 3 , and Clare L. Scott 1 , 2 , 8 ABSTRACT High-grade epithelial ovarian carcinomas containing mutated BRCA1 or BRCA2 (BRCA1/2 ) homologous recombination (HR) genes are sensitive to platinum-based chemotherapy and PARP inhibitors (PARPi), while restoration of HR function due to secondary mutations in BRCA1/2 has been recognized as an important resistance mechanism. We sequenced core HR pathway genes in 12 pairs of pretreatment and postprogression tumor biopsy samples collected from patients in ARIEL2 Part 1, a phase II study of the PARPi rucaparib as treatment for platinum-sensitive, relapsed ovar- ian carcinoma. In 6 of 12 pretreatment biopsies, a truncation mutation in BRCA1, RAD51C, or RAD51D was identifi ed. In fi ve of six paired postprogression biopsies, one or more secondary mutations restored the open reading frame. Four distinct secondary mutations and spatial heterogeneity were observed for RAD51C . In vitro complementation assays and a patient-derived xenograft, as well as predictive mole- cular modeling, confi rmed that resistance to rucaparib was associated with secondary mutations. SIGNIFICANCE: Analyses of primary and secondary mutations in RAD51C and RAD51D provide evidence for these primary mutations in conferring PARPi sensitivity and secondary mutations as a mechanism of acquired PARPi resistance. PARPi resistance due to secondary mutations underpins the need for early delivery of PARPi therapy and for combination strategies. Cancer Discov; 7(9); 984–98. ©2017 AACR. See related commentary by Domchek, p. 937. See related article by Quigley et al., p. 999. See related article by Goodall et al., p. 1006. 1 Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Cancer Centre, Melbourne, Victoria, Australia. 19 Centre for Cancer Research, Australia . 2 Department of Medical Biology, The University of Melbourne, Mel- University of Sydney at Westmead Millennium Institute, and Departments bourne, Victoria, Australia. 3 Clovis Oncology, Inc., Boulder, Colorado. 4 British of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Columbia Cancer Agency, Vancouver, British Columbia, Canada. 5 Stanford Uni- Australia. 20 QIMR Berghofer Medical Research Institute, Brisbane, Queens- versity, Palo Alto, California. 6 University of Washington, Seattle, Washington. land, Australia. 21 Mayo Clinic Cancer Center, Rochester, Minnesota. 22 Institute 7 Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom. 8 Australia. Department of Medical Oncology, Peter MacCallum Cancer Centre, Note: Supplementary data for this article are available at Cancer Discovery 9 Melbourne, Victoria, Australia. Developmental Biology Program, Memorial Online (http://cancerdiscovery.aacrjournals.org/). Sloan Kettering Cancer Center, New York, New York. 10 Department of Micro- biology and Molecular Genetics, University of Pittsburgh School of Medicine, O. Kondrashova, M. Nguyen, K. Shield-Artin, K.K. Lin, and Clare L. Scott Pittsburgh, Pennsylvania. 11 The University of Texas MD Anderson Cancer contributed equally to this article. Center, Houston, Texas. 12 Institut Bergonié, Bordeaux, France. 13 University Corresponding Author : Clare L. Scott, Walter and Eliza Hall Institute of Medi- of New South Wales and Prince of Wales Hospital, Sydney, New South Wales, cal Research, 1G Royal Parade, Parkville, Victoria 3052, Australia. Phone: Australia. 14 Flinders University, Adelaide, South Australia, Australia. 15 The 61-3-9345-2498; Fax: 61-3-9347-0852; E-mail: [email protected] 16 Ohio State University, James Cancer Center, Columbus, Ohio. Princess Mar- doi: 10.1158/2159-8290.CD-17-0419 garet Cancer Centre, University Health Network, Toronto, Ontario, Canada. 17 Foundation Medicine, Inc., Cambridge, Massachusetts. 18 Peter MacCallum © 2017 American Association for Cancer Research. 984 | CANCER DISCOVERY SEPTEMBER 2017 www.aacrjournals.org Downloaded from cancerdiscovery.aacrjournals.org on September 27, 2021. © 2017 American Association for Cancer Research. 14-CD-17-0419_p984-998.indd 984 8/18/17 2:30 PM Published OnlineFirst June 6, 2017; DOI: 10.1158/2159-8290.CD-17-0419 Secondary Mutations in RAD51C and RAD51D RESEARCH BRIEF INTRODUCTION with platinum-sensitive, relapsed high-grade epithelial ovar- ian carcinoma treated with rucaparib in ARIEL2 Part 1. Sam- The hallmark of synthetic lethality is the requirement for ples were assessed using targeted next-generation sequencing two complementary hits that, although tolerated individu- (NGS) with Foundation Medicine’s T5 assay, which sequences ally, result in cancer cell death when they occur together. A 287 cancer-related genes, including core HR pathway genes prime example is the observation that cells tolerate PARP (Supplementary Fig. S1; Supplementary Table S1; ref. 9). In 6 inhibition or homologous recombination (HR) impairment of the 12 cases, a deleterious mutation causing early protein individually, but cancer cells with impaired HR are killed by termination in an HR pathway gene (four in BRCA1 and one PARP inhibitors (PARPi), reflecting drug-induced inhibition each in RAD51C and RAD51D; five germline and one somatic of PARP1 catalytic activity, trapping of PARP1 at sites of DNA mutation) was detected in either an archival tumor sample damage, and/or alterations in the balance between error-free (n = 6) and/or screening biopsy sample (n = 4) prior to initia- and error-prone repair pathways (1–5). tion of rucaparib treatment (Table 1). All six patients with HR An exquisite proof of synthetic lethality comes from high- pathway genes mutated in their ovarian carcinoma derived grade epithelial ovarian carcinomas with mutated BRCA1 clinical benefit from rucaparib (four with a confirmed RECIST or BRCA2 (BRCA1/2) that are sensitive to platinum-based PR and two with SD; progression-free survival (PFS) ranged chemotherapy and PARPi (6–9). Furthermore, somatic rever- from 9.6 to 22.0 months). In a seventh case, a somatic CDK12 sion mutations in either BRCA1/2 following exposure of ovar- mutation (c.264delC) was identified with no additional muta- ian carcinoma to platinum-based chemotherapy or PARPi tions detected in the postprogression biopsy. CDK12 has been are identified as a mechanism of resistance. First reported in reported to affect transcription of multiple HR genes, although 2008 in a human pancreatic cell line and human ovarian carci- it is yet to be established as a core HR pathway gene (25, 26). noma (10, 11), secondary mutations that restore the wild-type In five of six cases with HR pathway gene mutations, postpro- BRCA2 open reading frame were detected in clinical ovarian gression biopsy samples contained at least one secondary muta- carcinoma, with a higher rate in women with platinum-resist- tion that was not detected in the pretreatment carcinomas. ant ovarian carcinoma who had prior chemotherapy (12, These secondary mutations restored the open reading frame of 13). More recently, examination of multiple tumor deposits the HR genes and thus potentially restored HR function and at autopsy revealed additional evidence of BRCA2 reversion conferred resistance to rucaparib (Table 1). Secondary muta- mutations and intrapatient heterogeneity with 12 distinct tions were identified only in postprogression cases with HR reversion events observed in a single patient with end-stage gene mutations (P = 0.015, Fisher exact test). In case 2, the only BRCA2-mutant ovarian carcinoma who had received multiple case in which no secondary HR gene mutation was detected in chemotherapy regimens (14). To date, most of the secondary the postprogression biopsy sample, the possibility of a rever- BRCA1/2 mutations are documented after platinum-chemo- sion mutation to wild-type sequence was unlikely, because the therapy exposure, with only limited reports after PARPi (15). wild-type allele frequency observed was not higher than expected Identification of patients with wild-typeBRCA1/2 but HR- based on the estimated tumor purity. The secondary muta- defective ovarian carcinoma is important, as these patients tions detected in the BRCA1-mutated cases were large in-frame may potentially respond to PARPi therapy. Germline or deletions (ranging from 123 to 861 bp) that restored the open somatic mutations in core HR genes beyond BRCA1/2, reading frame either by deleting the primary frameshift muta- although individually rare, collectively occur in 7% to 8% of tion (cases 1 and 3) or by shifting the reading frame back into ovarian
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